Parameter estimation techniques have been utilized in the development of a methodology to noninvasively measure blood perfusion using a new thermal surface probe. The core of this probe is comprised of a small, lightweight heat flux sensor that is placed in contact with tissue and provides time-resolved signals of heat flux and surface temperature while the probe is cooled by air jets. Parameter estimation techniques were developed that incorporate heat flux and temperature data with calculated data from a biothermal model of the tissue and probe. The technique simultaneously estimates blood perfusion and thermal contact resistance between the probe and tissue. Validation of this concept was carried out by experimentation with controlled flow through nonbiological porous media. Warm water was circulated through a fine pore sponge to provide a phantom model for blood perfusion through biological tissue. The parameter estimation technique was applied to measurements taken over a range of flow rates. Heat flux and temperature measurements and the resulting perfusion estimates correlated well with the experimentally imposed perfusion rate. This research helps establish the validity of using this method to develop a practical, noninvasive probe to clinically measure blood perfusion.